* [[Haynes:GalaxyChiP | ChIP in GALAXY]] - How to use GALAXY and a large BED file from your hard drive to create a track for the UCSC browser. Useful for data that is too large to create a custom track directly on the UCSC website.

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* [[Haynes:ChIPDataMining1 | ChIP on Promoters]] - How to find chromatin protein enrichment at gene promoters of interest for small sets of genes or all 23,000 human genes, using public ChIP data

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* [[Haynes:GOEnrichment | Gene Ontology Term Enrichment]] - How to compute which standardized terms (GO terms) for cell behavior/ biology are significantly over-represented in a user-defined list of genes

Dissolve Tris base in 200 mL dH<sub>2</sub>O (in a beaker with stirring). Add (by pipetting) glacial acetic acid and EDTA. Transfer solution to a graduated cylinder and fill up to 500 mL with dH<sub>2</sub>O. Transfer to a screw-cap bottle, loosen the cap and secure it to the bottle with autoclave tape. Autoclave in a pan filled about 2 in. deep with water (to prevent boiling-over) to sterilize.

Bioinformatics

ChIP in GALAXY - How to use GALAXY and a large BED file from your hard drive to create a track for the UCSC browser. Useful for data that is too large to create a custom track directly on the UCSC website.

ChIP on Promoters - How to find chromatin protein enrichment at gene promoters of interest for small sets of genes or all 23,000 human genes, using public ChIP data

Gene Ontology Term Enrichment - How to compute which standardized terms (GO terms) for cell behavior/ biology are significantly over-represented in a user-defined list of genes

Add FBS and pen-strep directly to the incomplete medium in the original stock bottle. Cap and invert to mix. Filter sterilize using a vacuum filtration unit.

Oligo Annealing Buffer, 10x[show][hide]

Formula: [1M NaCl; 100 mM Tris-HCl pH 7.4]
Volume: 1000 μL

5M NaCl, 200 μL

1M Tris-HCl, 100 μL

dH2O, 700 μL

Keep frozen at -20°C.

Tris-acetate-EDTA (TAE) Buffer, 50x[show][hide]

Formula: [2 M Tris, 1 M acetate, 50 mM EDTA]
Volume: 500 mL

Tris base (FW 121.14), 121 g

Glacial acetic acid, 28.55 mL

500 mM EDTA, 50 mL

Dissolve Tris base in 200 mL dH2O (in a beaker with stirring). Add (by pipetting) glacial acetic acid and EDTA. Transfer solution to a graduated cylinder and fill up to 500 mL with dH2O. Transfer to a screw-cap bottle, loosen the cap and secure it to the bottle with autoclave tape. Autoclave in a pan filled about 2 in. deep with water (to prevent boiling-over) to sterilize.